Friday, May 31, 2013

It's time to share the results of the School Malaise Trap program with the schools and the rest of the world. All participating teachers will receive an email this afternoon with a big results package.

You might remember that the program involved 60 schools in 42 cities. That is 77 classrooms with 2003 students that had a chance to learn a bit about DNA Barcoding and contribute to a large scale project aiming to catalog Canada's insect biodiversity. A total of 81 traps were running from April 22 to May 3 which was very early in the season. Actually the week before we had a major ice storm in Ontario.

The trap catches were quite high for early in the spring season. The 81 traps on average collected 1,180 specimens for the collecting period. Our staff sorted 95,500 specimens and selected 22,646 to be barcoded. Our final dataset was made up of 19,501 DNA Barcodes (not all worked and short barcodes were discarded). An impressive number of 1,392 putative species were collected over the two week period of the program. Here a breakdown:

276 of these species were new to BOLD which could either mean that they are known but have not been sampled yet or that they are indeed new to the region or even to science. That is now a job for the taxonomists were are working with. DNA Barcoding worked as a first proxy and now all those specimens in question will be looked at with an expert eye. Eventually some of them will get a species name.

The results were pretty amazing and that is reason enough to 'annoy' you with a series of blog posts over the next few days.

It is Julius Richard Petri's 161th birthday and Google honors him and his work with an animated Google Doodle. Make sure to hit the play button and after the bacteria have grown go over the Petri dishes with you cursor.

The German microbiologist invented the standard culture dish while he was working as an assistant in the lab of Robert Koch. He refined the technique of agar culture to clone bacterial colonies from single cells.

Wednesday, May 29, 2013

Two subspecies of bison (Bison bison) have been described for North America. Plains bison (Bison bison bison) and wood bison (Bison bison athabascae). These subspecies designations were based on morphology (skull and horn measurements, body proportions and size, as well as hair patterns),
but there was no consensus on if those subspecies are actually valid. Especially genetic studies have provide no support for plains bison and wood bison being subspecies.

To be frank, I am very critical of the entire subspecies concept, and so far I was not able to find anything that justifies yet another category between species and populations. It is often defined as a taxonomic division of a species which usually arises as a consequence of geographical isolation within that species. I don't see the difference to population in this case and no objective criterion has been brought forward so far.

Good to know that I am not alone with my rejection of the concept. Here is what colleague Matthew Cronin from the University of Alaska, Fairbanks has to say:

The scientific community has debated the whole subspecies category and
many if not most population geneticists like myself recognize the entire
category has been used very subjectively, in other words, people have
designated subspecies without a lot of rigorous scientific evidence.
And that’s been going on since the late 1800s, so there’s a lot of
subspecies for which there hasn’t been adequate analysis.

Cronin and colleagues have done a comparative assessment of bison and cattle subspecies by analyzing the microsatellite
variation within and between the putative bison
subspecies, and compared those levels of genetic divergence with those of
cattle
breeds and subspecies. No matter if one accepts or rejects the subspecies ranking per se bison subspecies
are currently recognized by management agencies, e.g. Wood Bison are currently listed as threatened under the US Endangered Species Act.

The results of the study discount the existence of bison subspecies. The data show no phylogenetic distinction of extant wood bison and plains bison. They actually show less divergence of microsatellite allele frequencies than cattle breeds and subspecies. Furthermore, in Wood Buffalo National Park both were mixed and the researchers couldn't find any wood bison without some degree
of plains bison ancestry. Consequently extant wood bison herds should be considered a
northwestern subpopulation of the North American bison.

These results have ramifications for policies concerning the management
and conservation of bison populations. Both Canada
and the United States maintain gene banks to
conserve germplasm and tissue for agriculturally useful species
including bison,
and both countries have initiated collections of
bison tissues. The results of this study will be used in further
development
of germplasm acquisition for bison and suggest that
plains bison and wood bison should be considered geographic populations
and not subspecies. Regarding management of wild
bison populations, they could be managed to maintain phenotypic
characteristics
of interest, as is done with cattle breeds. That
is, wood bison can be managed as a geographic subpopulation to maintain
morphological
characters (whether heritable or environmentally
induced) or other potentially unique traits. However, the lack of
subspecies-level
differentiation suggests that managers of wild and
domestic populations could interbreed wood bison and plains bison to
maintain
or enhance genetic variation and reduce the
potential for genetic defects and reduced fitness resulting from
inbreeding.

Tuesday, May 28, 2013

Potato flea beetles (genus Epitrix) are known to be serious pests of a wide variety of vegetable crops. Aside from potatoes infestations can occur in tomato, pepper, eggplant, bean, cabbage, corn, cucumber, lettuce and spinach. Damage results through feeding, causing numerous holes in the leaves or the potato itself. This injury eventually kills infested leaves. In addition, potato flea beetles may transmit early blight. In severe cases, the plant can die or production can be strongly diminished emphasizing the importance of scouting and control.

A group of French researchers now propose DNA Barcoding as a tool to reliably identify all developmental stages of the most economically important Epitrix species feeding on potato in Europe and North America (Epitrix cucumeris, Epitrix similaris, Epitrix tuberis, Epitrix subcrinita and Epitrix hirtipennis). The researchers started with testing two different markers (COI and ITS2) for their suitability to differentiate Epitrix species. Both worked fine which is good news for the standard DNA Barcode region COI. Consequently they developed an RFLP-based diagnostic method and showed that unambiguous species discrimination can be achieved by using the restriction enzyme TaqI on COI polymerase chain reaction products. This is very good news as it represents a significant reduction of processing time and cost. Such a RFLP-based DNA Barcoding tool may allow for more extensive sampling and regular monitoring.

Coincidentally there were some new developments on the regulatory level in Europe:

During the final stages of review of this manuscript, the European commission published a decision (212/270/EU) to prevent the introduction of Epitrix tuberis and Epitrix subcrinita in Europe and limit the spread of Epitrix cucumeris and Epitrix similaris. By enabling the identification of Epitrix specimens at different periods of the life cycle, this diagnostics tool should help member states conducting survey for the presence of potato flea beetles on potato crops as well as other host plant species, as recommended by the European commission. Fast and accurate detection of Epitrix potato flea beetles would help study their potential spread and contribute to their management with minimal disruption to Solanaceae trade.

Monday, May 27, 2013

In 2008 Mackenzie Cowell and Jason Bobecreated DIYbio.org an organization dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biology professionals. In so-called "biohacklabs", such as Genspace, amateur biologists can come together to create projects, whether just for fun, but also to improve their knowledge or engage in existing projects contributing to current research efforts.

The movement now spawned another community supported Do-It-Yourself (DIY) biology laboratory now in Seattle, Washington. Financed by crowfunding, grants and membership fees the community lab HiveBio will be opening soon and allow amateurs to do e.g. DNA analysis that used to be the domain of professional researchers. Anyone 16 or older will be able to use the lab if they pay HiveBio's membership fee (as low as $50 a month) or a $15 drop-in fee.

It has been repeatedly shown how inclusive DNA Barcoding can be when it comes to citizen science and there are already projects at Genspace that take advantage of the fact that is has become so accessible (and to some extend affordable).

In addition to providing a lab space HiveBio focuses some of its resources on proliferating science education in the Pacific Northwest. Classes, conducted on a volunteer basis by members, are held on a monthly basis at the lab. The long-term goal of the education branch of HiveBio is to expand the education opportunities to include classes taught off-site at educational institutions throughout Seattle. These classes will be offered for a minimal fee.

One major objective of the organization is inclusivity. HiveBio keeps the cost of membership as low as possible in order to be accessible to citizen scientists of a wide array of incomes. It is the intention of the organization to attract individuals of all education levels, from PhD to entry level science enthusiasts. Housing a wide array of knowledge is central to the theme of proliferating science knowledge. Members will be both learning and teaching in this context. We believe that diversity is a key elements of science innovation.

HiveBio is also interested in providing a pathway to scientific publication for its members. In addition to providing the space and equipment necessary for research, HiveBio will provide members with information on the steps and protocol required for scientific publication.

Just an excerpt of their objectives which I find very promising. What all these new entities need aside from money and supplies is buy in from us researchers. I know that many colleagues are hesitant and skeptical about amateur-driven science but I believe they underestimate the power of dedication and the willingness of people to become so deeply involved in a project simply because they have access to the same tools we use. Actually any such project has much more academic freedom than professional research that is often limited by funding, personal career planning, policy, and sometimes governmental strategy.

This new
effort represents an undergraduate extension of the NSF-funded Barcoding Life’sMatrix program – a research education project that engages a national network
of high schools in building the DNA Barcode reference library. Although the project was originally established
by CMB as a discovery science-based
model to enhance teaching and learning in high school settings, it has
attracted widespread interest from college faculty who seek new opportunities
to bridge research and undergraduate science education through student
participation in iBOL. The assembly and
submission of validated reference barcode records by undergraduates will be aided
by BOLD-SDP, the customized student interface to the Barcode of Life Data Systems
that was formally launched in spring 2013.

This pilot effort is supported by the U.S. Department of Education, and by a CA state grant. grant details: [Achieving a
Collaborative College Education through STEM Opportunities (Project ACCESO),
Title V, Hispanic-Serving Institutions STEM Grant] to CSUCI, and [California Community
Colleges Economic and Workforce Development: Applied Biotechnologies
(12-317-038)] to NVBC.

Thursday, May 23, 2013

A global committee of taxonomists announced its list of top 10 species
from 2012 today. Each year, the International Institute for Species Exploration (IISE) at Arizona State University international committee of taxon experts evaluates
the hundreds of new species that have been nominated by the public,
IISE staff, scientists, scientific journal editors and by the committee
members themselves.

And here we go - the top 10 with short descriptions by the IISE:

Lilliputian VioletViola lilliputana
Country: Peru

Tiny violet:
Not only is the Lilliputian violet among the smallest violets in the
world, it is also one of the most diminutive terrestrial dicots. Known
only from a single locality in an Intermontane Plateau of the high Andes
of Peru, Viola lilliputana lives in the dry puna grassland eco-region.
Specimens were first collected in the 1960s, but the species was not
described as a new until 2012. The entire above ground portion of the
plant is barely 1 centimeter tall. Named, obviously, for the race of
little people on the island of Lilliput in Jonathan Swift’s Gulliver’s
Travels.

Carnivorous sponge:
A spectacular, large, harp- or lyre-shaped carnivorous sponge
discovered in deep water (averaging 3,399 meters) from the northeast
Pacific Ocean off the coast of California. The harp-shaped structures or
vanes number from two to six and each has more than 20 parallel
vertical branches, often capped by an expanded, balloon-like, terminal
ball. This unusual form maximizes the surface area of the sponge for
contact and capture of planktonic prey.

Old World monkey:
Discovered in the Lomami Basin of the Democratic Republic of the Congo,
the lesula is an Old World monkey well known to locals but newly known
to science. This is only the second species of monkey discovered in
Africa in the past 28 years. Scientists first saw the monkey as a
captive juvenile in 2007. Researchers describe the shy lesula as having
human-like eyes. More easily heard than seen, the monkeys perform a
booming dawn chorus. Adult males have a large, bare patch of skin on the
buttocks, testicles and perineum that is colored a brilliant blue.
Although the forests where the monkeys live are remote, the species is
hunted for bush meat and its status is vulnerable.

No to the Mine! SnakeSibon noalamina
Country: Panama

Snail-eating snake:
A beautiful new species of snail-eating snake has been discovered in
the highland rainforests of western Panama. The snake is nocturnal and
hunts soft-bodied prey including earthworms and amphibian eggs, in
addition to snails and slugs. This harmless snake defends itself by
mimicking the alternating dark and light rings of venomous coral snakes.
The species is found in the Serranía de Tabasará mountain range where
ore mining is degrading and diminishing its habitat. The species name is
derived from the Spanish phrase “No a la mina” or “No to the mine.”

A Smudge on Paleolithic ArtOchroconis anomala
Country: France

Fungus:
In 2001, black stains began to appear on the walls of Lascaux Cave in
France. By 2007, the stains were so prevalent they became a major
concern for the conservation of precious rock art at the site that dates
back to the Upper Paleolithic. An outbreak of a white fungus, Fusarium
solani, had been successfully treated when just a few months later,
black staining fungi appeared. The genus primarily includes fungi that
occur in the soil and are associated with the decomposition of plant
matter. As far as scientists know, this fungus, one of two new species
of the genus from Lascaux, is harmless. However, at least one species of
the group, O. gallopava, causes disease in humans who have compromised
immune systems.

World’s Smallest VertebratePaedophryne amanuensis
Country: New Guinea

Tiny frog:
Living vertebrates — animals that have a backbone or spinal column —
range in size from this tiny new species of frog, as small as 7
millimeters, to the blue whale, measuring 25.8 meters. The new frog was
discovered near Amau village in Papua, New Guinea. It captures the title
of ‘smallest living vertebrate’ from a tiny Southeast Asian cyprinid
fish that claimed the record in 2006. The adult frog size, determined by
averaging the lengths of both males and females, is only 7.7
millimeters. With few exceptions, this and other ultra-small frogs are
associated with moist leaf litter in tropical wet forests — suggesting a
unique ecological guild that could not exist under drier circumstances.

Endangered ForestEugenia petrikensis
Country: Madagascar

Endangered shrub:
Eugenia is a large, worldwide genus of woody evergreen trees and shrubs
of the myrtle family that is particularly diverse in South America, New
Caledonia and Madagascar. The new species E. petrikensis is a shrub
growing to two meters with emerald green, slightly glossy foliage and
beautiful, dense clusters of small magenta flowers. It is one of seven
new species described from the littoral forest of eastern Madagascar and
is considered to be an endangered species. It is the latest evidence of
the unique and numerous species found in this specialized, humid forest
that grows on sandy substrate within kilometers of the shoreline. Once
forming a continuous band 1,600 kilometers long, the littoral forest has
been reduced to isolated, vestigial fragments under pressure from human
populations.

Lightning Roaches?Lucihormetica luckae
Country: Ecuador

Glow-in-the-dark cockroach:
Luminescence among terrestrial animals is rather rare and best known
among several groups of beetles — fireflies and certain click beetles in
particular — as well as cave-inhabiting fungus gnats. Since the first
discovery of a luminescent cockroach in 1999, more than a dozen species
have (pardon the pun) “come to light.” All are rare, and interestingly,
so far found only in remote areas far from light pollution. The latest
addition to this growing list is L. luckae that may be endangered or
possibly already extinct. This cockroach is known from a single specimen
collected 70 years ago from an area heavily impacted by the eruption of
the Tungurahua volcano. The species may be most remarkable because the
size and placement of its lamps suggest that it is using light to mimic
toxic luminescent click beetles.

No Social ButterflySemachrysa jade
Country: Malaysia

Social media lacewing:
In a trend-setting collision of science and social media, Hock Ping
Guek photographed a beautiful green lacewing with dark markings at the
base of its wings in a park near Kuala Lumpur and shared his photo on
Flickr. Shaun Winterton, an entomologist with the California Department
of Food and Agriculture, serendipitously saw the image and recognized
the insect as unusual. When Guek was able to collect a specimen, it was
sent to Stephen Brooks at London’s Natural History Museum who confirmed
its new species status. The three joined forces and prepared a
description using Google Docs. In this triumph for citizen science,
talents from around the globe collaborated by using new media in making
the discovery. The lacewing is not named for its color — rather for
Winterton’s daughter, Jade.

Hanging Around in the JurassicJuracimbrophlebia ginkgofolia
Country: China

Hangingfly fossil:
Living species of hangingflies can be found, as the name suggests,
hanging beneath foliage where they capture other insects as food. They
are a lineage of scorpionflies characterized by their skinny bodies, two
pairs of narrow wings, and long threadlike legs. A new fossil species,
Juracimbrophlebia ginkgofolia, has been found along with preserved
leaves of a gingko-like tree, Yimaia capituliformis, in Middle Jurassic
deposits in the Jiulongshan Formation in China’s Inner Mongolia. The two
look so similar that they are easily confused in the field and
represent a rare example of an insect mimicking a gymnosperm 165 million
years ago, before an explosive radiation of flowering plants.

Wednesday, May 22, 2013

In 1993 the United Nations proclaimed May 22 the International Day for Biological Diversity (IDB) to increase understanding and awareness of biodiversity issues. The aim of the day is to promote the need for preservation of our planet, and in this context to make sure that the biodiversity that populates it remains just that, diverse.

The loss of too many species potentially destroys the fragile system that keeps our planet healthy and functional. That's why the Convention on Biological Diversity was created as an internationally legally binding treaty. The three main goals of the Convention are:

conservation of biological diversity,

sustainable use of its components and ,

fair and equitable sharing of benefits arising from genetic resources.

Water sustains all life on Earth. It is vital for all people and ultimately determines our way of life. Providing and sustaining water for the needs of people around the world is already well recognized as a major challenge for sustainable development in most areas in both developed and developing countries. The ecosystems of our world, but particularly forests and wetlands, ensure that clean water is available to human communities. Water in turn underpins all ecosystem services.

Wetlands can help reduce risks from flooding. Restoring soils can reduce erosion and pollution and can increase water available for crops. Protected areas can assist in providing water to cities. These are but a few examples of how ecosystem management can help us solve water-related problems.

Education and public awareness represent a substantial part of the Convention and events such as Biodiversity Day, awareness of global issues and concerns can be raised. It is a good opportunity to educate the general public on things that can be done to rectify or reduce these issues. If you want to know what is going on in your country on this day have a look at this page.

Tuesday, May 21, 2013

Few species reside solely in the location where they originated. In fact, the migration of species is a predominant feature of life on Earth. Species expand, contract and shift their geographical distributions constantly. It is our perception of these ecosystems and the boundaries in time and space that we draw around them that makes us discriminate between native and non-native species - a fully arbitrary process. Nevertheless, we have become very concerned about recent species invasions mainly because of the tremendous damage some non-native species can cause to ecological systems, our health, and our economy.

Although many species have been introduced outside of their home ranges, relatively few introduced species become abundant and widespread in the new ranges. Identifying the mechanisms driving profound invasions when they do occur is the focus of a large body of research in invasion biology. It has long been assumed the worst invasive species have an "away-field advantage." meaning they succeed because they do better in their new territories than they do at home. They escape their natural enemies, use novel weapons and defense mechanisms on unsuspecting natives and generally outcompete local flora and fauna by disrupting the balance of the existing ecosystem.

Although their data generally support the idea that invasive species exhibit increased performance in their introduced range, roughly half of the species investigated performed similarly between the home and away ranges. One implication of this finding is that novel ecological and evolutionary conditions in the introduced range may only partly explain success in a new range. Indeed, there has been much recent progress in determining the traits that make some species invasive across a range of environmental conditions, with growing evidence that many successful introduced species share similar traits with successful native species. The authors conclude that species' traits, and particularly the interaction between traits and environmental context, may be a better predictor of invasion success than novel conditions alone.

Friday, May 17, 2013

The genus Anopheles comprises about 460 species. Over 100 can transmit human malaria, but only 30–40 commonly transmit parasites of the genus Plasmodium, which cause malaria in humans. The major vector of malaria in India, Anopheles fluviatilishas been described as a complex of three closely related species, named as S, T and U, based on variations in chromosomal inversions. Over-sized chromosomes, so called polytene chromosomes, have developed from standard chromosomes and are commonly found in the salivary glands of flies (and their close relatives, the mosquitoes). These polytene chromosomes are also used to identify species e.g. of Chironomid larvae that are notoriously difficult to identify. This method is not free of error and researchers have been trying to find reliable DNA markers that confirm the species S, T, U in the case of Anopheles fluviatilis. Two DNA regions (ITS2 and the D3 region of 28S) had been used by some researchers whereas others showed that both show insufficient variation and in one case even a 100% similarity to another congener Anopheles minimus.

A group of colleagues from India have now published a study that shows that two members of this 'species complex' rather represent genetically con-specific intermixing populations with negligible genetic differentiation. The third 'species' had previously been shown to be a phenotypic variant of Anopheles minimus. The authors used DNA Barcoding and contrasted the results with those from the other two markers and found very little variation in the barcode region and cross-reactivity in one of the other markers (ITS2). Some of the specimens couldn't be assigned to either subgroup as both 'species' variants were found in some individuals.

Very interesting study also in line with the fact that all supposed species were capable of carrying the parasite.

Wednesday, May 15, 2013

Lichens are symbiotic organisms consisting of a fungus and a partner capable of photosynthesis either either a green alga or cyanobacterium. The body of most lichens is different from those of its partners growing separately. The fungus
surrounds the algal cells, often enclosing them within complex fungal
tissues unique to lichen associations. In many species the fungus
even penetrates the algal cell wall. The lichen association is a close symbiosis and extends the ecological range of both partners. However, is not always
obligatory for their growth and reproduction in natural environments. Especially the algae can live independently.

Lichens are commonly used to monitor ecosystem health and the impact of
atmospheric pollution. In addition, some lichens are potentially
valuable sources of pharmaceutical products, including antibiotics,
and antioxidants. Despite their occurrence in all terrestrial
ecosystems and their overall ecological importance, lichens are commonly
overlooked. Furthermore, robust species delimitation and accurate identification remains challenging. There are more than 18, 000 currently accepted species of lichen-forming fungi and an estimated diversity of more than 28, 000 species. On the other hand the number of photosynthetic partners is very low (usually only two genera).

A new study now presents reference sequences using the fungal ITS marker as a DNA Barcode for identifying species within a species complex (Rhizoplaca melanophthalma). Overall, the study demonstrates the potential for accurately identifying lichen species by using DNA Barcoding to identify the lichen-forming fungi. The researchers also formally describe five new species within the group they studied.

Their conclusion:

As molecular sequence data become more readily available, they will
allow us to better understand the diversity of lichenized fungi. Their
use in identifying species will become increasingly important and
routinely applied. Other disciplines such as ecology, conservation and
physiology will benefit from a more objectively based species
circumscription, enabling us to interpret distribution and ecological
patterns better and more accurately monitor environmental disturbance
and climate change.

Tuesday, May 14, 2013

Contemporary collections of sponges in the Indo-west Pacific have escalated substantially due to pharmaceutical discovery, national bioregional planning, and compliance with international conventions on the seabed and its marine genetic resources beyond national jurisdictions. These partially processed operational taxonomic unit (OTU) collections now vastly outweigh the expertise available to make them better 'known' via complete taxonomy, yet for for many bioregions they represent the most significant body of current available knowledge. Increasing numbers of cryptic species, previously undetected morphologically, are now being discovered by molecular and chemical analyses. The uncoordinated and fragmented nature of many collections, however, means the knowledge and expertise gained from a particular project are often lost to future projects without a biodiversity informatics legacy.

This is the first part of the abstract of a paper that was recently published in Integrative and Comparative Biology. The SpongeMaps Project represents a legacy of the Marine Barcoding project (MarBOL)which I ledover the four year of its existence. While the DNA Barcoding activities will carry on as part of iBOL other sub-projectshave been finished. The SpongeMaps project was intended to provide an online collaborative platform to integrate morphometric data with DNA Barcodes and other DNA fragments that were generated as part of the Porifera Tree of Life (PorTol). Over time it evolved into a workspace focusing on specimen data that are aggregated into OTUs. It contains all infrastructure to compare images, descriptions, distribution, and chemical components. The approach has some similarities to the BOLD BIN pages (sponge example here) but is certainly more specialized and detailed when it comes to the peculiarities of sponges. By June 2013, 50 000 georeferenced specimens will be online together with 60 000 images (photosin situ, on deck, of preserved specimens, light micrographs, SEMs, line drawings, and sketches). All that will be connected to geographical and genetic data.

SpongeMaps can generate output data in a format that is useful for the Encyclopedia of Life (EOL) and the Atlas of living Australia (ALA) by producing individual ‘‘species-pages’’ that are published directly to both online portals.

Monday, May 13, 2013

Friday, May 10, 2013

In 541 AD, eight centuries before the Black Death, a deadly infectious disease hit the Byzantine Empire, reaching Constantinople in 542 and North Africa, Italy, Spain, and the French-German border by winter 543. The so called “Plague of Justinian”, named after the contemporaneous emperor, led to mass mortality in Europe similar to that of the Black Death. It persisted in the territory of the Roman Empire until the middle of the 8th century and likely contributed to its decline, shaping the end of antiquity.

Based on historic records it had been assumed this Justinian plague was similar to the bubonic plague that struck Europe eight centuries later. However, some discrepancies between historical accounts and the progression of infections with the bacterium that causes the plague (Yersinia pestis) caused considerable debate among scientists about whether it is the same disease or a completely different infection. This was further complicated by the fact that the origin of the disease was unknown, although it is thought to have arrived from Egypt through trade ships.

A new study now confirmedunambiguously that Yersinia pestis was indeed the causing agend of this first pandemic. The researchers used ancient DNA analyses on samples obtained from an early medieval cemetery in Achheim in Bavaria, Germany. By using both quantitative Real-Time PCR and a conventional PCR approach they amplified and sequenced a 70 bp portion and a 133 bp fragment of the Yersinia pestis-specific plasminogen activator gene (pla). This gene, which is specific to Yersinia pestis, has been used in previous studies to test samples from plague skeletons dating to the time of the Black Death. The group was also able track down the origins of this plague. As for the second and third pandemic, the original sources of the bacillus were in Asia.

The question remains if at Justinian times only one strain or several were introduced to Europe. The latter was the case for the Black Death in the 14th century.

Amazing what a couple of bones are able to tell us more than 1400 years after they were buried.

Thursday, May 9, 2013

Florida Fish and Wildlife Conservation Commission researchers say they've discovered a new species of fish in the southeastern U.S. They first noticed a new DNA profile (unfortunately they don't say which gene region they've used) while testing a bass specimen from the Chipola River in 2007 as part of a broader genetic study of bass. After confirming the initial discovery the researchers searched for similar DNA profiles in bass caught in nearby rivers to determine the fish's range. They found the Choctaw bass in coastal rivers in Alabama and along the western Florida panhandle, including Choctawhatchee River.

The Choctaw bass is morphologically very similar to the spotted bass (Micropterus punctatus), and that's why no one had previously distinguished the two different species, in spite of decades of bass research. Have a look at both images and see for yourself. Only by counting scales, fin rays and gill rakers one will perhaps be able to tell them apart - or simply by using DNA Barcoding.

Micropterus punctatus (Spotted bass)

The new fish's name was chosen because its range overlaps with the historic range of the Native American Choctaw. "Haiaka" is a Choctaw word meaning "revealed" or "manifest".

Tuesday, May 7, 2013

The wheat curl mite, Aceria tosichella (Eriophyoidea), is widely
distributed worldwide and has a broad host range that
includes most cereals and several native and introduced grasses. Unless found in extremely high numbers, wheat curl mites generally cause little
direct damage in the field other than the characteristic leaf curling
and the occasional trapping of the flag leaf. However, both immature and
adult wheat curl mite transmit Wheat Streak Mosaic Virus.

The majority of eriophyoid species are actually known to be highly host-specific; thus the wide host range exhibited by Aceria tosichella (more than 80 species) has long been regarded as an anomaly. More recent research in Australia showed that there are actually at least two local lineages with overlapping geographical
distributions and that only one of them is implicated in Wheat Streak Mosaic Virus transmission.

Now a group of reasearchers from Poland collected morphologically similar Aceria tosichella populations from only
five host plants in a small area of western Poland. They used DNA Barcoding and the nuclear D2 region of 28S rDNA to assess genetic lineages and test if Aceria tosichella reallyis a single, highly polyphagous species.

Their study reveals that the wheat curl mite is composed of several discrete genetic lineages with variable host ranges and therefore variable pest
potential, indicating not only the likely existence of a cryptic species
complex, but also the potential for more genetic and host-range
diversity if populations are sampled over a broader area on more of
the approximately 80 recorded host plants for this species. Only two lineages in the present study appear to have high pest potential on cereals (one specifically for barley), whereas several others appear to specialize on wild grass species.

There is a lot left to do in order to find out which lineage is harmful and which not. At least we have a good idea on how to do it.

Monday, May 6, 2013

In 1996 a shipwreck was discovered during a survey of the Dor lagoon on the Israeli Mediterranean coast, south of Haifa. Based on some metal objects and Carbon14 tests of some organic materials, the so called Tantura F shipwreck was dated to the 7-8th centuries AD which is known to be the region’s Early Islamic period.

Among the findings were eight amphorae made of Nile Delta silt with resinous linings. The 6-7-liter amphorae contained bones from all parts of the fish skeleton, indicating that the amphorae once contained whole fish. Preliminary morphological analysis of the bones at the University of Haifa assigned the fish to the genus Tilapia but a group of researchers wanted to confirm the species identities and used short DNA Barcodes (mini-barcodes) to find out which load the ship had carried 1400 years ago.

Given the age of the samples they could only retrieve a 140bp fragment which didn't allow a full species designation but the fact that on this length there was only one bp difference to the two Tilapia species Oreochromis aureus and Sarotherodon galilaeus (transition from G to A) certainly confirms the intitial identification. The authors speculate that the ancient fish belonged to an extinct species or sub-species closely related to the two contemporary species. I find that a bit of a stretch given the short length of the sequences. One nucleotide difference on a length of 140bp. That makes perhaps 5 on the entire DNA Barcode region assuming equal distribution of mutations (unlikely, but for this little exercise it will do). That is probably half a percent divergence. Among fishes that rarely qualifies for different species.

That should not divert from the results as such. I find it pretty cool that DNA Barcoding can help with archeology. Let's not forget that the amphorae contained all parts of the fish skeleton which makes identification by morphology possible. Imagine you only have one little fragment.

Friday, May 3, 2013

With coastlines on the Pacific and Atlantic Oceans, Andean mountains,
and Amazon basins, Colombia’s landscapes are vast and vastly diverse.
Here, where the Pacific, Amazonian, Caribbean, and Orinoquian lowland
regions meet, the landscapes are a patchwork of mangroves, snow-capped
peaks, grasslands, deserts, wetlands, rainforests, dry forests, cloud
forests, and other habitats. While world-renowned for its richness in
bird species, Colombia also has an extraordinary diversity of amphibians
and mammals, as well as orchids and butterflies.

However, human induced deforestation
has already substantially changed the Andean landscape in Colombia. It
is also linked to the conversion of lowland tropical forests to palm oil plantations. However, compared to neighboring countries rates of deforestation in Colombia are still relatively low. Other challenges are caused by natural factors such as the
geological instability related to Colombia's position along the Pacific
Ring of Fire. Colombia has 15 major volcanoes, the eruptions of which have on occasion resulted in substantial loss of life. Geological faults that have caused numerous devastating earthquakes.
Heavy floods both in mountainous areas and in low-lying watersheds and
coastal regions regularly occur during the rainy seasons with varying rainfall intensities due to the El Niño-Southern Oscillation.

Colombian researchers have been part of DNA Barcoding studies e.g. on amphibians, mosquitoes, or plants. They are leads of important initiatives to help build the global library of DNA Barcodes (e.g. ArBOL, ColdCode). It is estimated that Colombia might be the home to 150,000 to 200,000 species. About 1000 of them are barcoded (mostly lepidoptera, amphibians, and birds). A lot left to do but I am sure Colombia will catch up very quickly.

Thursday, May 2, 2013

Are you still watching the stars with your new telescope? I bet you can see what I see outside the windows
of my TARDIS. The star you're searching for is still there, it just tends to
fall out of view occasionally.

Do you remember how you always said how you'd love to be
travelling with me again through the skies? I envy you right now, living on
this wonderful planet in your lovely little house treating yourself to a flask
of tea on your porch while you look at the stars. They're beautiful, I
would know, I live amongst them and I've traveled to so many. I’ve seen
galaxies born and fading away.

But what is it with your little blue planet that makes me
coming back so often? Is it its people
that are so brilliant and clever and funny and everything I'd ever want in companions?
I don’t know and that means a lot to somebody who has been at the beginning
and the end of the universe. Or maybe it’s the way how life evolved since the
days your planet was not more than just another rock in a sidearm of an inconspicuous
galaxy.

I have so much enjoyed reading about the old thinkers such as Huxley, Williams, Bintliff and Gould, and this new book on randomness in evolution. Marc Srour is not the only one wondering why there is such a kerfuffle about this as evolution has a significant random component. Mutations can be random, genetic drift is random and there is hopefully no doubt that both play a big role in the evolution of species. Well, there is but don't get me started on this group of inveterate ignorants. You have a couple of eloquent, outspoken, wise proponents of reason that can deal with them much better. By the way, don't miss this one:

It's sort of quiet...The TARDIS and I have decided to be
alone for a while. Don't want to cause too much trouble (you are very good in that without me)! We also have a paradox to solve. Who is she?